Utility of ITS and rbcL Sequences for Resolving Intraspecific Divergence in Saccharum spontaneum L

Abstract Saccharum spontaneum L., commonly known as wild sugarcane or kans grass, is a close wild relative of sugarcane, representing the majority of terrestrial environments from the open ground to the shoreline. Due to its diverse applications as food, fodder, food ingredients, medicine, household products, pulp material, and even religious offerings, understanding the genetic relationships among populations is crucial. The present study attempted to understand the phylogenetic and evolutionary relationships of six field samples and two commercial samples from the chosen population of S. spontaneum in Tamil Nadu. The genomic material was extracted and amplified using nuclear ribosomal DNA internal transcribed spacer (nrDNA-ITS) and ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) sequences and compared with those obtained from the NCBI database. The evolutionary history was inferred using MEGA11 software. The results showed that the presence of highly conserved sites in the rbcL region led to a close phylogenetic relationship falling under a common clade, which could be useful for molecular identification of this species. On the other hand, ITS markers were found to be useful for determining the phylogeny of S. spontaneum via both phenetic and cladistic approaches. The ITS region in this wild sugarcane has better discrimination ability despite the highly conserved sites with few rapidly evolving sites. Four of the collected specimens showed a close relationship, along with two commercial specimens, suggesting shared adaptations or a common geographic origin. Additionally, two other populations were found to have diverged from the rest of the specimens, exhibiting low genetic distance, indicating recent evolutionary divergence.